I think so too. They wouldn't just leave Cortana's absence open-ended like that. I bet it would have done wonders for the Flood elements of the sandbox having them potentially be at the center of the game, as opposed to the Sangheili and Jiralhanae-led Covenants. As a side plot they could have had us return to Sanghelios or other colonies as the Arbiter to expel the Covenant.